Mass spectrometers typically comprise an ion source where an analyte is ionised and extracted to pass to a mass analyser. Ion optics controls the passage of ions through the mass spectrometer. The ion path between ion source and mass analyser may include one or more ion traps/ion stores, and may also include a further mass analyser. Such a further mass analyser is often used for the rapid acquisition of pre-scans (i.e. low resolution mass spectra used for initial identification of ions). The other mass analyser tends to be of a higher resolution.
In its broadest sense, this invention relates to mass spectrometry that makes selective use of a reaction cell to alter a population of ions to be analysed. The “reaction” may be any act that changes the ion population such as mass filtering, introducing other ions, fragmenting ions, causing the ions to react to form new molecular species, or changing the energy or charge state of the ions to name but a few examples. Of course, combinations of the above may also be performed in the reaction cell. Often, it is desirable to collect mass spectra from both the unreacted ions and the product ions. This allows difference spectra to be derived such that product ions are easily identified.
In traditional tandem mass spectrometers, the reaction cell also resides on the ion path between ion source and high-resolution mass analyser. As a result, all ions must pass through the reaction cell to reach the high-resolution mass spectrometer. If a mass spectrum from the precursor ions is required, the reaction cell must be inactivated. Often, a mass spectrometer will be continually switched between acquisition of mass spectra from precursor and product ions such that operation of the reaction cell must also be switched continually between reacting and non-reacting. At best, this introduces a time delay and ion losses; at worst (e.g. for reactions with reactive gas), such switching is impossible on the time scale of analysis.
To provide a specific context for this invention, there follows a brief discussion of tandem mass spectrometry. Tandem mass spectrometry comprises the fragmentation of precursor ions in a reaction cell. Fragmentation may be effected in a number of ways, e.g. electron capture dissociation (ECD), collision induced dissociation (CID), photon induced dissociation (PID), surface induced dissociation (SID), electron transfer dissociation (ETD), etc. In tandem mass spectrometry, in the narrow meaning of this term, there is only one stage of fragmentation so that spectra are taken from precursor and first-generation fragment ions. However, further stages of fragmentation may be performed such that the fragment ions may themselves be fragmented. This is referred to as MSn spectrometry, with n referring to the level of selection such that tandem mass spectrometry corresponds to MS2.
Typical tandem mass spectrometers are disclosed in papers like Hunt D F, Buko A M, Ballard J M, Shabanowitz J, and Giordani A B; Biomedical Mass Spectrometry, 8 (9) (1981) 397-408 (both precursor and fragments are selected by quadrupoles); H. R. Morris, T. Paxton, A. Dell, J. Langhorne, M. Berg, R. S. Bordoli, J. Hoyes and R. H. Bateman; Rapid Comm. in Mass Spectrom; 10 (1996) 889-896 and numerous patents such as U.S. Pat. No. 6,285,027B1 (wherein precursors are selected by a quadrupole and fragments are analysed using time-of-flight (TOF) analyser). Each of these mass spectrometers has a fragmentation cell disposed on the ion path between ion source and mass analyser. Therefore, the reaction cell must be made inactive when mass spectra are required from the precursor ions. In CID, this necessitates evacuating the collision gas from the fragmentation cell which is a time-consuming process.
Higher throughput of fragmentation is provided in US 2002/115,056, US 2002/119,490 and US 2002/168,682, wherein ion fragmentation is performed for all precursors in parallel and specificity is sacrificed in favour of speed.
U.S. Pat. No. 6,586,727 proposes a compromise where, for collection of spectra from fragment ions, the reaction cell is operated to favour fragmentation and, for collection of spectra from precursor ions, the reaction cell is operated to reduce fragmentation. The spectra taken from precursor and fragment ions respectively are searched for fragment ions of interest or for precursor/fragment peak pairs separated by a predetermined neutral loss. Identified pairs may be chosen for subsequent tandem mass spectrometry. For reliable identification, m/z for both precursor and fragment mass peaks must be determined with accuracy of several parts per million. Therefore such parallel-processing methods require the use of accurate-mass analysers such as FT ICR, single- or multiple-reflection TOFs, orbitrap, etc., all of which operate in a substantially pulsed manner. However, the continuous ion beam that exits the reaction cell in U.S. Pat. No. 6,586,727 is sampled by an orthogonal acceleration TOF analyser with quite low transmission and duty cycle, so sensitivity of the method gets compromised. Also, the layout of the mass spectrometer precludes it from acquiring precursor spectra while fragmentation is carried out (which could be very advantageous for relatively slow fragmentation methods such as ETD, ECD, IRMPD). Generally linear geometry of such instruments makes installation of such novel methods quite difficult and prone to compromising analytical performance.
WO97/48120 describes a tandem mass spectrometer that uses a time of flight (TOF) mass analyser. A reaction cell is provided, unusually located beyond the TOF analyser. Precursor ions are generated by an ion source, kicked sideways into the TOF analyser to be reflected by an ion mirror. Where a mass spectrum of the precursor ions is required, the ion mirror is operated to reflect the precursor ions to be incident on the detecting element of the TOF analyser. Where fragment ions are of interest, the ion mirror is operated to reflect ions to miss the detecting element and instead exit the TOF analyser and enter a reaction cell where they are fragmented. The fragment ions are ejected from the reaction cell back into the TOF analyser where the ion mirror is operated to reflect the fragment ions to be incident on the detecting element. Although this geometry offers greater flexibility in the design and operation of the reaction cell, its utility is limited because of high ion losses caused by the low duty cycle of orthogonal pulsing.
The above mass spectrometers suffer from a number of problems, in addition to the problem of switching between fragmenting/non-fragmenting modes already described. Spectra are acquired from all fragment ions at the same time. Consequently, the fragment spectra become very crowded and this limits the number of precursor/fragment pairs that will be found. In addition, this also adversely affects the dynamic range of ion intensities that may be addressed in the search (i.e. low-intensity precursor peaks might go unnoticed).